At the begining of the movie, the body of the event horizon captain is floating around on the bridge, with his skin cut to pieces and no clothes on. Yet later on during the movie, when Lt Peters bumps into his body he has a uniform on!!!!

This isn't a slip up. That wasn't the captain at the beginning of the movie, It was Dr Weir. Remember at the end of the movie he was like that when the ship brought him back?
If you watch the scene more carefully you will notice that the very next shot is of Dr Weir waking up. The body you saw spinning was in fact a bad dream warning Weir of what's going to happen...you may also notice that the ship's window is broken in the background, caused by Dr Weir when he shoots the Rivet gun through the window, further proof that this is not the captain.